Variant report

Variant	rs6927023
Chromosome Location	chr6:28454221-28454222
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28451721..28454293-chr6:28455250..28457902,2	MCF-7	breast:
2	chr6:28364266..28370257-chr6:28453674..28463075,14	K562	blood:

Variant related genes	Relation type
ENSG00000158691	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10080420	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10434846	0.81[ASN][1000 genomes]
rs10733177	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10755647	0.81[ASN][1000 genomes]
rs10807032	0.81[ASN][1000 genomes]
rs10807040	0.81[ASN][1000 genomes]
rs1150715	0.80[ASN][1000 genomes]
rs1150722	0.83[ASN][1000 genomes]
rs1150725	0.80[ASN][1000 genomes]
rs11758055	0.81[ASN][1000 genomes]
rs1225600	0.80[ASN][1000 genomes]
rs12332986	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1600621	0.80[ASN][1000 genomes]
rs1778510	0.80[ASN][1000 genomes]
rs2057295	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2108924	1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2191036	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394119	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2799076	0.83[ASN][1000 genomes]
rs28382606	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28475822	0.80[ASN][1000 genomes]
rs2859375	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs34358978	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34931542	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3757180	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs381493	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs384399	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3852211	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs389603	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs394772	0.81[ASN][1000 genomes]
rs399558	1.00[EUR][1000 genomes]
rs3999023	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs402426	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs404343	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs408255	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs411538	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4121090	0.81[ASN][1000 genomes]
rs418628	0.81[ASN][1000 genomes]
rs418898	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs420436	0.81[ASN][1000 genomes]
rs420463	0.81[ASN][1000 genomes]
rs422089	1.00[EUR][1000 genomes]
rs424426	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs426922	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs429875	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs434636	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs442174	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs443924	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs449074	0.81[ASN][1000 genomes]
rs454746	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4711176	0.81[ASN][1000 genomes]
rs4713172	0.81[ASN][1000 genomes]
rs4713174	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55860825	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6456812	1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6456817	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6456820	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456829	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6456832	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6456833	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6899512	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901001	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6902583	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[ASN][1000 genomes]
rs6906826	0.81[ASN][1000 genomes]
rs6908459	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6910120	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6912921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6918631	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6922161	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[ASN][1000 genomes]
rs6922302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6923163	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6925972	0.81[ASN][1000 genomes]
rs6929449	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6935589	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6937042	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6938371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6941222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7381746	0.81[ASN][1000 genomes]
rs7382159	0.81[ASN][1000 genomes]
rs7382309	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7382583	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7739305	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7752448	1.00[JPT][hapmap]
rs7752721	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7759855	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs7761914	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7767897	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[ASN][1000 genomes]
rs7771490	0.81[ASN][1000 genomes]
rs7773193	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs911177	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9295769	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9295770	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9393922	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9393923	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9461450	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9461452	0.80[ASN][1000 genomes]
rs9461453	0.80[ASN][1000 genomes]
rs9461457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9461464	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9468328	0.80[ASN][1000 genomes]
rs9468335	0.80[ASN][1000 genomes]
rs9468337	0.80[ASN][1000 genomes]
rs9468341	0.80[ASN][1000 genomes]
rs9468375	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9468384	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468394	0.81[ASN][1000 genomes]
rs9654587	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6927023	ZSCAN16	cis	lymphoblastoid	seeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28443200-28456600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:28451800-28456800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:28453600-28456600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:28453800-28454800	Enhancers	K562	blood

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